03.01Structural switching regions by ASP :
The program ASP (MM Young, K Kirshenbaum, KA Dill & S Highsmith) is run by default. ASP predicts structural switches, i.e. regions that are likely to undergo controlled conformational rearrangements. The output is reported only if one or more such regions are predicted

09.00Secondary structure and solvent accessibility by PROFsec and PROFacc :
The program new programs PROFsec and PROFacc are run upon request. They replace the PHD series in that prediction accuracy is higher. Although more accurate, we currently do not run the PROF programs by default due to a lack of CPU resources.

02.00cysteine bonding partners by CYSPRED :
The program CYSPRED (P Fariselli, P Riccobelli &amp R Casadio) is run by default. CYSPRED predicts cysteins that are likely to be partners in cysteine bridges. The output is reported only if at least one cystein is predicted to bind.

Volker Eyrich (Columbia Univ., Chemistry Dept.) has written a general interface that enables users to simultaneously submit a sequence to a wide variety of prediction services (submission page). The following services are available at the moment:

Miscellaneous services

SignalP prediction of presence and location of signal peptide cleavage sites in amino acid sequences from different organisms

04.99Low-complexity regions by SEG (default,
example):
The program SEG (J C Wootton & S Federhen) is executed, by default. SEG scans your sequence for regions of low-complexity ('simple sequences' or 'composition-biased regions'). You may turn this default off by using the keyword 'no seg in any line before the one beginning with a hash ('#').

03.99Filtering your alignment (default):
Your alignment will be filtered before running PHD, in order to reduce possible redundancy. You may turn this default off by using the keyword 'no filter.

04.98Return no seg
('return no seg') The string "return no seg" in any line before the one starting with a hash (#) results in that SEG results are not returned.

04.99Store results here, return no mail output
('return no mail') The string "return no mail" in any line before the one starting with a hash (#) results in that we shall not returned the results by mail. Instead, the results for your requests will be stored on our machines for 3 days, and you will receive a mail that simply tells you how you can ftp the result from here. The reason for including this option is that some requests may result in very large output files, and those may be difficult to handle for your local mailing device (in particular when you request HTML formatted output).

04.99Return output in HTML format
('return html') The string "return html" in any line before the one starting with a hash (#) results in that the email you get will have the entire results attached in one HTML formatted file (which you can load into any WWW browser).
The conversion of the old format to the new one is still rather rudimentary. However, thanks to the program MView (Nigel Brown, MRC, Mill Hill, London) part of the output is already much easier to digest in this new format!

04.99Return output in HTML format for printouts
('perline=60') The strings "return html60" OR "perline=N" (with N=1..number of residues of your protein) in any line before the one starting with a hash (#) result in that the email you get will have the all output attached in one HTML formatted file (to display with any WWW browser) that has fewer characters per line than the normal HTML output (see "return HTML"), so that you can print the output. (For further information see the option "return html".)

04.99Return output in HTML format (with PHD graphics)
('return html detail') The string "return html detail" in any line before the one starting with a hash (#) results in that the email you get will have the entire results attached in one HTML formatted file (which you can load into any WWW browser), furthermore, the PHD predictions will also be displayed graphically.
Note: the HTML files resulting from the PHD predictions may be large. To avoid that your mail will be too big, you may therefore use the option of leaving the result on our machines, and simply ftp it to your local machine (see option "return no mail").

04.99Return output (with PHD graphics) in HTML format for printouts
('perline=60') The strings "return html detail 60" OR "perline=N" (with N=1..number of residues of your protein) in any line before the one starting with a hash (#) result in that the email you get will have the all output attached in one HTML formatted file (to display with any WWW browser) that has fewer characters per line than the normal HTML output (see "return HTML detail"), so that you can print the output. (For further information see the option "return html".)
Note: the HTML files resulting from the PHD predictions may be large. To avoid that your mail will be too big, you may therefore use the option of leaving the result on our machines, and simply ftp it to your local machine (see option "return no mail").

03.99 Your input sequence by its SWISSPROT identifier
('# swissid') You can submit your sequence through its SWISS-PROT identifier. The string "# SWISSID" prompts the system to interpret the following line to be an identifier of the form 'name_species' (example for input). NOTE: only identifiers in our current SWISS-PROT release are valid.

03.99 Your input sequence(s) by FASTA alignment
('do not align') You can submit your alignment in FASTA format. This requires two keywords: (1) the string "# FASTA list" prompts the system to interpret your alignment as one in the FASTA format (specification and example for FASTA list format), and (2) the keyword "do NOT align" in a line before the one starting with a hash ('#'), assures that your alignment will not be re-aligned (as for the options of submitting your sequences via FASTA format).

03.99 Your input sequence(s) by PIR alignment
('do not align') You can submit your alignment in PIR format. This requires two keywords: (1) the string "# PIR list" prompts the system to interpret your alignment as one in the PIR format (specification and example for PIR list format), and (2) the keyword "do NOT align" in a line before the one starting with a hash ('#'), assures that your alignment will not be re-aligned (as for the options of submitting your sequences via PIR format).

04.98Coiled-coil regions: now by default the program COILS written by Andrei Lupas is run on your sequence. An output is returned if a coiled-coil region has been detected.

04.98Functional sequence motifs: now by default the PROSITE database written by Amos Bairoch, Philip Bucher and Kay Hofmann is scanned for sequence motifs. An output is returned if any motif has been detected.

The neural network prediction of transmembrane helices (PHDhtm) is refined by a dynamic programming-like algorithm. This method resulted in correct predictions of all transmembrane helices for 89% of the 131 proteins used in a cross-validation test; more than 98% of the transmembrane helices were correctly predicted. The output of this method is used to predict topology, i.e., the orientation of the N-term with respect to the membrane. The expected accuracy of the topology prediction is > 86%. Prediction accuracy is higher than average for eukaryotic proteins and lower than average for prokaryotes. PhdTopology is more accurate than all other methods tested on identical data sets (Rost, Casadio & Fariselli, Protein Science, 1996).

New defaults

03.96:
For predicting the locations of transmembrane helices, PHDhtm is used. The more accurate refined version along with the prediction of topology (PHDtopology) is available upon request ('predict htm topology').